-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_13066573-13248644

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_30966-T1
Valid prediction for HiQ_model.g20660.t1
Valid prediction for GeneMark_model.53373_t
Couldn't classify 162489, 162984
Sorry, prediction pasa_asmbl_9004.p1 fails validation.
(TCC)	 TG	162489-162984	GT	TCG
(TCC)	 AG	163083-163222	GT	TGG
(GCA)	 AG	163389-163472	GT	GGG
(CTG)	 AG	163631-163873	CC	GAC
-recovered pasa_asmbl_9004.p1, terminal, 163631, 163873
-recovered pasa_asmbl_9004.p1, internal, 163083, 163222
-recovered pasa_asmbl_9004.p1, internal, 163389, 163472
Valid prediction for GlimmerHMM_glimmerT_30959-T1
Valid prediction for snap_scaffold_12-snap.2468-T1
Valid prediction for snap_scaffold_12-snap.2443-T1
Valid prediction for GeneMark_model.53397_t
Valid prediction for GlimmerHMM_glimmerT_30942-T1
Valid prediction for Augustus_model.g20656.t1
Valid prediction for snap_scaffold_12-snap.2431-T1
Valid prediction for GeneMark_model.53364_t
Valid prediction for snap_scaffold_12-snap.2434-T1
Valid prediction for GeneMark_model.53399_t
Valid prediction for GeneMark_model.53374_t
Valid prediction for GeneMark_model.53392_t
Valid prediction for Augustus_model.g20655.t1
Valid prediction for GeneMark_model.53362_t
Valid prediction for snap_scaffold_12-snap.2437-T1
Valid prediction for GlimmerHMM_glimmerT_30955-T1
Valid prediction for GlimmerHMM_glimmerT_30962-T1
Valid prediction for GeneMark_model.53381_t
Valid prediction for GeneMark_model.53354_t
Valid prediction for snap_scaffold_12-snap.2453-T1
Valid prediction for snap_scaffold_12-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_30954-T1
Valid prediction for GeneMark_model.53383_t
Valid prediction for Augustus_model.g20654.t1
Valid prediction for snap_scaffold_12-snap.2460-T1
Valid prediction for snap_scaffold_12-snap.2459-T1
Valid prediction for snap_scaffold_12-snap.2451-T1
Valid prediction for GeneMark_model.53384_t
Valid prediction for snap_scaffold_12-snap.2452-T1
Valid prediction for snap_scaffold_12-snap.2467-T1
Valid prediction for snap_scaffold_12-snap.2465-T1
Valid prediction for GeneMark_model.53396_t
Valid prediction for GeneMark_model.53387_t
Valid prediction for snap_scaffold_12-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_30958-T1
Valid prediction for GlimmerHMM_glimmerT_30950-T1
Valid prediction for Augustus_model.g20650.t1
Valid prediction for GeneMark_model.53372_t
Valid prediction for snap_scaffold_12-snap.2446-T1
Valid prediction for GeneMark_model.53386_t
Valid prediction for GeneMark_model.53369_t
Valid prediction for GlimmerHMM_glimmerT_30946-T1
Valid prediction for GeneMark_model.53390_t
Valid prediction for GlimmerHMM_glimmerT_30939-T1
Valid prediction for snap_scaffold_12-snap.2454-T1
Valid prediction for Augustus_model.g20641.t1
Valid prediction for GeneMark_model.53356_t
Valid prediction for GeneMark_model.53394_t
Valid prediction for Augustus_model.g20649.t1
Valid prediction for GlimmerHMM_glimmerT_30963-T1
Valid prediction for GlimmerHMM_glimmerT_30952-T1
Valid prediction for Augustus_model.g20647.t1
Valid prediction for GeneMark_model.53402_t
Valid prediction for snap_scaffold_12-snap.2433-T1
Valid prediction for Augustus_model.g20644.t1
Valid prediction for GeneMark_model.53389_t
Valid prediction for GeneMark_model.53365_t
Valid prediction for GeneMark_model.53380_t
Valid prediction for GeneMark_model.53378_t
Valid prediction for snap_scaffold_12-snap.2463-T1
Valid prediction for GlimmerHMM_glimmerT_30953-T1
Valid prediction for GeneMark_model.53352_t
Valid prediction for GlimmerHMM_glimmerT_30960-T1
Valid prediction for GeneMark_model.53400_t
Valid prediction for GeneMark_model.53370_t
Valid prediction for GeneMark_model.53367_t
Valid prediction for GeneMark_model.53360_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.53395_t
Valid prediction for Augustus_model.g20643.t1
Couldn't classify 9819, 9987
Couldn't classify 12012, 12298
Sorry, prediction pasa_asmbl_8063.p1 fails validation.
(GAT)	 CA	9819-9987	GT	CTG
(CGG)	 AG	10271-10457	GT	AGG
(TGA)	 AG	10916-11138	GT	AGG
(GTC)	 AG	11255-11342	GT	AGG
(GCC)	 AG	11584-11649	GT	TGG
(CCC)	 AG	12012-12298	GT	AGG
-recovered pasa_asmbl_8063.p1, internal, 10271, 10457
-recovered pasa_asmbl_8063.p1, internal, 10916, 11138
-recovered pasa_asmbl_8063.p1, internal, 11255, 11342
-recovered pasa_asmbl_8063.p1, internal, 11584, 11649
-recovered pasa_asmbl_8063.p1, internal, 12012, 12298
Valid prediction for Augustus_model.g20651.t1
Valid prediction for snap_scaffold_12-snap.2455-T1
Couldn't classify 126489, 126656
Sorry, prediction pasa_asmbl_8053.p1 fails validation.
(ATG)	 TA	123023-123161	GT	AGG
(CTG)	 AG	125516-125658	GT	AGG
(GGG)	 AG	126489-126656	GT	ACG
-recovered pasa_asmbl_8053.p1, initial, 123023, 123161
-recovered pasa_asmbl_8053.p1, internal, 125516, 125658
-recovered pasa_asmbl_8053.p1, internal, 126489, 126656
Valid prediction for GeneMark_model.53371_t
Valid prediction for GeneMark_model.53366_t
Valid prediction for GlimmerHMM_glimmerT_30949-T1
Valid prediction for GlimmerHMM_glimmerT_30944-T1
Valid prediction for GlimmerHMM_glimmerT_30948-T1
Valid prediction for GeneMark_model.53401_t
Valid prediction for GeneMark_model.53377_t
Valid prediction for GlimmerHMM_glimmerT_30956-T1
Couldn't classify 135601, 136329
Sorry, prediction pasa_asmbl_8050.p1 fails validation.
(ATG)	 AA	135601-136329	CA	CCC
Valid prediction for Augustus_model.g20657.t1
Valid prediction for snap_scaffold_12-snap.2450-T1
Valid prediction for snap_scaffold_12-snap.2449-T1
Valid prediction for HiQ_model.g20645.t1
Couldn't classify 81182, 81203
Sorry, prediction pasa_asmbl_8057.p1 fails validation.
(CCA)	 GG	81182-81203	GT	GGG
(CCA)	 AG	81912-82084	GT	AGG
(GTG)	 AG	82304-82444	GT	AGG
(GTT)	 AG	83049-83177	AA	GAA
-recovered pasa_asmbl_8057.p1, terminal, 83049, 83177
-recovered pasa_asmbl_8057.p1, internal, 81912, 82084
-recovered pasa_asmbl_8057.p1, internal, 82304, 82444
Valid prediction for snap_scaffold_12-snap.2435-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_10414-T1
Valid prediction for CodingQuarry_transcript_10415-T1
Valid prediction for HiQ_model.g20652.t1
Valid prediction for GlimmerHMM_glimmerT_30947-T1
Valid prediction for GeneMark_model.53359_t
Valid prediction for GeneMark_model.53357_t
Valid prediction for HiQ_model.g20659.t1
Valid prediction for GlimmerHMM_glimmerT_30943-T1
Valid prediction for snap_scaffold_12-snap.2444-T1
Valid prediction for GeneMark_model.53353_t
Valid prediction for snap_scaffold_12-snap.2448-T1
Valid prediction for snap_scaffold_12-snap.2441-T1
Valid prediction for GeneMark_model.53363_t
Valid prediction for Augustus_model.g20658.t1
Valid prediction for snap_scaffold_12-snap.2458-T1
Valid prediction for pasa_asmbl_8061.p1
Valid prediction for Augustus_model.g20662.t1
Valid prediction for snap_scaffold_12-snap.2445-T1
Valid prediction for GlimmerHMM_glimmerT_30957-T1
Valid prediction for Augustus_model.g20648.t1
Valid prediction for GeneMark_model.53398_t
Valid prediction for pasa_asmbl_8048.p1
Valid prediction for GlimmerHMM_glimmerT_30940-T1
Valid prediction for GeneMark_model.53375_t
Valid prediction for snap_scaffold_12-snap.2461-T1
Valid prediction for GeneMark_model.53391_t
Valid prediction for GeneMark_model.53403_t
Valid prediction for GeneMark_model.53379_t
Valid prediction for HiQ_model.g20653.t1
Valid prediction for GeneMark_model.53385_t
Valid prediction for GeneMark_model.53355_t
Valid prediction for snap_scaffold_12-snap.2442-T1
Valid prediction for GeneMark_model.53382_t
Valid prediction for snap_scaffold_12-snap.2436-T1
Valid prediction for GeneMark_model.53361_t
Valid prediction for GeneMark_model.53358_t
Valid prediction for GeneMark_model.53388_t
Valid prediction for snap_scaffold_12-snap.2466-T1
Couldn't classify 13667, 13799
Sorry, prediction pasa_asmbl_8062.p3 fails validation.
(CAG)	 CA	13667-13799	GT	GGG
(GTG)	 AG	14428-14738	GG	GAG
-recovered pasa_asmbl_8062.p3, terminal, 14428, 14738
Valid prediction for GeneMark_model.53368_t
Valid prediction for GlimmerHMM_glimmerT_30961-T1
Valid prediction for Augustus_model.g20642.t1
Valid prediction for snap_scaffold_12-snap.2447-T1
Valid prediction for Augustus_model.g20646.t1
Valid prediction for GlimmerHMM_glimmerT_30941-T1
Valid prediction for GeneMark_model.53393_t
Valid prediction for snap_scaffold_12-snap.2456-T1
Valid prediction for CodingQuarry_transcript_10413-T1
Valid prediction for GlimmerHMM_glimmerT_30951-T1
Valid prediction for GeneMark_model.53376_t
Valid prediction for GlimmerHMM_glimmerT_30964-T1
Valid prediction for snap_scaffold_12-snap.2432-T1
Valid prediction for snap_scaffold_12-snap.2439-T1
Valid prediction for Augustus_model.g20661.t1
Valid prediction for GlimmerHMM_glimmerT_30965-T1
Valid prediction for GlimmerHMM_glimmerT_30945-T1
Valid prediction for snap_scaffold_12-snap.2438-T1
Valid prediction for snap_scaffold_12-snap.2464-T1
Valid prediction for snap_scaffold_12-snap.2462-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14154, rend_intergenic: 10952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19645, rend_intergenic: 14987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75971, rend_intergenic: 68322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84029, rend_intergenic: 76073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105268, rend_intergenic: 102289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126078, rend_intergenic: 118304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129469, rend_intergenic: 126187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134029, rend_intergenic: 129817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142500, rend_intergenic: 140095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158566, rend_intergenic: 145634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179067, rend_intergenic: 168321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182072
-exon list size: 629


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
1.0    
1.1    
1.3    
1.4    
1.6    
1.7    
1.9    
2.1    
2.2    
2.4    
2.5    
2.7    
2.9    
3.0    
3.2    
3.3    
3.5    
3.6    
3.8    
4.0    
4.1    
4.3    
4.4    
4.6    
4.8    
4.9    
5.1    
5.2    
5.4    
5.5    
5.7    
5.9    
6.0    
6.2    
6.3    
6.5    
6.7    
6.8    
7.0    
7.1    
7.3    
7.4    
7.6    
7.8    
7.9    
8.1    
8.2    
8.4    
8.6    
8.7    
8.9    
9.0    
9.2    
9.4    
9.5    
9.7    
9.8    
10.0    
10.1    
10.3    
10.5    
10.6    
10.8    
10.9    
11.1    
11.3    
11.4    
11.6    
11.7    
11.9    
12.0    
12.2    
12.4    
12.5    
12.7    
12.8    
13.0    
13.2    
13.3    
13.5    
13.6    
13.8    
13.9    
14.1    
14.3    
14.4    
14.6    
14.7    
14.9    
15.1    
15.2    
15.4    
15.5    
15.7    
15.8    
16.0    
16.2    
16.3    
16.5    
16.6    
16.8    
17.0    
17.1    
17.3    
17.4    
17.6    
17.7    
17.9    
18.1    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.3    
19.5    
19.7    
19.8    
20.0    
20.1    
20.3    
20.4    
20.6    
20.8    
20.9    
21.1    
21.2    
21.4    
21.6    
21.7    
21.9    
22.0    
22.2    
22.3    
22.5    
22.7    
22.8    
23.0    
23.1    
23.3    
23.5    
23.6    
23.8    
23.9    
24.1    
24.2    
24.4    
24.6    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
26.9    
27.1    
27.3    
27.4    
27.6    
27.7    
27.9    
28.1    
28.2    
28.4    
28.5    
28.7    
28.8    
29.0    
29.2    
29.3    
29.5    
29.6    
29.8    
30.0    
30.1    
30.3    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.5    
31.7    
31.9    
32.0    
32.2    
32.3    
32.5    
32.6    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.8    
33.9    
34.1    
34.2    
34.4    
34.5    
34.7    
34.9    
35.0    
35.2    
35.3    
35.5    
35.7    
35.8    
36.0    
36.1    
36.3    
36.5    
36.6    
36.8    
36.9    
37.1    
37.2    
37.4    
37.6    
37.7    
37.9    
38.0    
38.2    
38.4    
38.5    
38.7    
38.8    
39.0    
39.1    
39.3    
39.5    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.7    
40.9    
41.0    
41.2    
41.4    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.6    
42.8    
42.9    
43.1    
43.3    
43.4    
43.6    
43.7    
43.9    
44.1    
44.2    
44.4    
44.5    
44.7    
44.8    
45.0    
45.2    
45.3    
45.5    
45.6    
45.8    
46.0    
46.1    
46.3    
46.4    
46.6    
46.8    
46.9    
47.1    
47.2    
47.4    
47.5    
47.7    
47.9    
48.0    
48.2    
48.3    
48.5    
48.7    
48.8    
49.0    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.0    
51.2    
51.3    
51.5    
51.7    
51.8    
52.0    
52.1    
52.3    
52.5    
52.6    
52.8    
52.9    
53.1    
53.2    
53.4    
53.6    
53.7    
53.9    
54.0    
54.2    
54.4    
54.5    
54.7    
54.8    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.3    
56.4    
56.6    
56.7    
56.9    
57.1    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.6    
58.8    
59.0    
59.1    
59.3    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.9    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 14154, rend_intergenic: 10952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19645, rend_intergenic: 14987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75971, rend_intergenic: 68322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84029, rend_intergenic: 76073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105268, rend_intergenic: 102289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126078, rend_intergenic: 118304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129469, rend_intergenic: 126187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134029, rend_intergenic: 129817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142500, rend_intergenic: 140095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158566, rend_intergenic: 145634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179067, rend_intergenic: 168321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support